Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes.

Jiao C, Gao M, Wang X, Fei Z - BMC Genomics (2015)

Bottom Line:
These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.The newly discovered genes from wild Vitis, as well as SNPs and small indels we identified, may facilitate future studies on the molecular mechanisms related to valuable traits possessed by these wild Vitis and contribute to the grape breeding programs.Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.

Background: Grape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production. Grape cultivars have been selected and evolved to produce high-quality fruits during their domestication over thousands of years. However, current widely planted grape cultivars suffer extensive loss to many diseases while most wild species show resistance to various pathogens. Therefore, a comprehensive evaluation of wild grapes would contribute to the improvement of disease resistance in grape breeding programs.

Results: We performed deep transcriptome sequencing of three Chinese wild grapes using the Illumina strand-specific RNA-Seq technology. High quality transcriptomes were assembled de novo and more than 93% transcripts were shared with the reference PN40024 genome. Over 1,600 distinct transcripts, which were absent or highly divergent from sequences in the reference PN40024 genome, were identified in each of the three wild grapes, among which more than 1,000 were potential protein-coding genes. Gene Ontology (GO) and pathway annotations of these distinct genes showed those involved in defense responses and plant secondary metabolisms were highly enriched. More than 87,000 single nucleotide polymorphisms (SNPs) and 2,000 small insertions or deletions (indels) were identified between each genotype and PN40024, and approximately 20% of the SNPs caused nonsynonymous mutations. Finally, we discovered 100 to 200 highly confident cis-natural antisense transcript (cis-NAT) pairs in each genotype. These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.

Conclusion: The three de novo assembled transcriptomes provide a comprehensive sequence resource for molecular genetic research in grape. The newly discovered genes from wild Vitis, as well as SNPs and small indels we identified, may facilitate future studies on the molecular mechanisms related to valuable traits possessed by these wild Vitis and contribute to the grape breeding programs. Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.

Mentions:
The assembled transcripts included redundant sequences, mainly due to alternative splicing. We found that 4.80% (BH), 6.81% (HN) and 8.94% (S) transcripts could be clustered with other transcripts (sequence identity ≥ 97% and overlap length ≥ 100 bp). Only one representative transcript from each cluster was used in the downstream functional enrichment/annotation analysis, to avoid the repetitive counting of the same genes. Finally, we obtained a total of 1,650-2,000 distinct unique transcripts in each of the three accessions. The coding potential of these transcripts was then assessed by Coding Potential Calculator (CPC) [34]. Consequently, we got 1,058, 1,296 and 1,315 distinct genes with high coding potential from BH, HN and S, respectively, as well as 596, 609, and 732 potential non-coding transcripts (Figure 2A). The list of these transcripts is provided in Additional file 2. We then performed the GO term enrichment analyses (corrected P-value ≤ 0.05) on these three distinct protein-coding gene datasets. A total of 19 GO terms under the category of biological process were enriched in distinct genes in all three accessions (Table 3 and Figure 2B), and the most representative GO term was response to stimulus (GO:0050896), which included nearly half of the distinct genes. Among the child terms of GO:0050896, the most significantly enriched one was defense response (GO:0006952; Table 3). We also identified 15, 18 and 30 enriched child GO terms associated with resistance-related biological processes in BH, HN and S, respectively (Additional file 3).Figure 2

Mentions:
The assembled transcripts included redundant sequences, mainly due to alternative splicing. We found that 4.80% (BH), 6.81% (HN) and 8.94% (S) transcripts could be clustered with other transcripts (sequence identity ≥ 97% and overlap length ≥ 100 bp). Only one representative transcript from each cluster was used in the downstream functional enrichment/annotation analysis, to avoid the repetitive counting of the same genes. Finally, we obtained a total of 1,650-2,000 distinct unique transcripts in each of the three accessions. The coding potential of these transcripts was then assessed by Coding Potential Calculator (CPC) [34]. Consequently, we got 1,058, 1,296 and 1,315 distinct genes with high coding potential from BH, HN and S, respectively, as well as 596, 609, and 732 potential non-coding transcripts (Figure 2A). The list of these transcripts is provided in Additional file 2. We then performed the GO term enrichment analyses (corrected P-value ≤ 0.05) on these three distinct protein-coding gene datasets. A total of 19 GO terms under the category of biological process were enriched in distinct genes in all three accessions (Table 3 and Figure 2B), and the most representative GO term was response to stimulus (GO:0050896), which included nearly half of the distinct genes. Among the child terms of GO:0050896, the most significantly enriched one was defense response (GO:0006952; Table 3). We also identified 15, 18 and 30 enriched child GO terms associated with resistance-related biological processes in BH, HN and S, respectively (Additional file 3).Figure 2

Bottom Line:
These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.The newly discovered genes from wild Vitis, as well as SNPs and small indels we identified, may facilitate future studies on the molecular mechanisms related to valuable traits possessed by these wild Vitis and contribute to the grape breeding programs.Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.

Background: Grape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production. Grape cultivars have been selected and evolved to produce high-quality fruits during their domestication over thousands of years. However, current widely planted grape cultivars suffer extensive loss to many diseases while most wild species show resistance to various pathogens. Therefore, a comprehensive evaluation of wild grapes would contribute to the improvement of disease resistance in grape breeding programs.

Results: We performed deep transcriptome sequencing of three Chinese wild grapes using the Illumina strand-specific RNA-Seq technology. High quality transcriptomes were assembled de novo and more than 93% transcripts were shared with the reference PN40024 genome. Over 1,600 distinct transcripts, which were absent or highly divergent from sequences in the reference PN40024 genome, were identified in each of the three wild grapes, among which more than 1,000 were potential protein-coding genes. Gene Ontology (GO) and pathway annotations of these distinct genes showed those involved in defense responses and plant secondary metabolisms were highly enriched. More than 87,000 single nucleotide polymorphisms (SNPs) and 2,000 small insertions or deletions (indels) were identified between each genotype and PN40024, and approximately 20% of the SNPs caused nonsynonymous mutations. Finally, we discovered 100 to 200 highly confident cis-natural antisense transcript (cis-NAT) pairs in each genotype. These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.

Conclusion: The three de novo assembled transcriptomes provide a comprehensive sequence resource for molecular genetic research in grape. The newly discovered genes from wild Vitis, as well as SNPs and small indels we identified, may facilitate future studies on the molecular mechanisms related to valuable traits possessed by these wild Vitis and contribute to the grape breeding programs. Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.